If I read the code correctly, this comes from the function prepare_link
in ocaml_compiler.ml which derives the dependencies from the files
.ml.depends and .mli.depends. But these files are not generated for
packs, hence the required dependencies are not build.

The attached small patch (patch-ocamlbuild-link-pack-deps.diff) simply
treats the .mlpack files as dependency files for packs, which fixes
the issue.

Additional Information

This byte-code linking problem with packs was reported to the list
two years ago, but with no answer: